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edeveaud:
Hello,

lib/README says that trollrop should be downloaded from http://gitorious.org/trollop/mainline/blobs/raw/master/lib/trollop.rb,
while post http://forum.x3dna.org/md-simulations/ruby-scripts-for-the-analysis-of-md-simulation-trajectories/msg538/#msg538 says from http://trollop.rubyforge.org/

trollrop is available from https://rubygems.org/gems/trollop/versions/

any recommendation about specific version to use ? v1.16.2 or newer version will fit the requirements ?

Eric

xiangjun:
Hi Eric,

Thank you so much for reporting the inconsistency issues with trollop.rb in 3DNA.


--- Quote ---lib/README says that trollrop should be downloaded from http://gitorious.org/trollop/mainline/blobs/raw/master/lib/trollop.rb,
--- End quote ---

The note was intended for myself, that I downloaded trollrop 1.16.2 using wget from that URL. The trollop.rb script is cleaned up (see below) and distributed with 3DNA, so users do not need a separate download.


--- Code: ---# Note from Xiang-Jun Lu (3dna.lu@gmail.com) -- some minor revisions:
#     o   reformatted the code, 4 spaces indent, split long lines
#     o   corrected '-h' or '--version' to '-v'
#     o   corrected 'In thise case' to 'this'
#     o   removed '=> e' to avoid warning on unsed variable
#     o   refined FLOAT_RE to allow for + before the number
#     o   added [INTEGER_RE = /^[+-]?\d+$/] to allow for negative integer
--- End code ---

To avoid confusions, the README file has been removed in the updated distribution of 3DNA v2.4.


--- Quote ---while post http://forum.x3dna.org/md-simulations/ruby-scripts-for-the-analysis-of-md-simulation-trajectories/msg538/#msg538 says from http://trollop.rubyforge.org/

trollrop is available from https://rubygems.org/gems/trollop/versions/
--- End quote ---

The post was dated on January 19, 2011, the URL for trollop was at the specific URL at that time. As you noticed, the URL for trollop has been changed again. Trollop may be relocated to yet another place (e.g., github) in the future.

Also, note that the 'trollop' gem has been deprecated and has been replaced by 'optimist'. In the 3DNA v2.4 distribution, the lib/trollop.rb single file is not a Rubygem dependency. It is a standalone "commandline option parser for Ruby that just gets out of your way." (http://manageiq.github.io/optimist/) It was for this simplicity that I initially picked up trollop from several other options. I've been happily using trollop since then in my Ruby scripts.


--- Quote ---any recommendation about specific version to use ? v1.16.2 or newer version will fit the requirements ?
--- End quote ---

The slightly revised version of trollop v1.16.2 distributed with 3DNA has been working well, as far as I am aware.

Best regards,

Xiang-Jun

PS. Did you tried 3DNA v2.4.1 with zsh and confirm that the x3dna_setup script works as expected, or otherwise?

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.

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